title: Loss of NAPRT1 expression by tumor-specific promoter methylation provides a novel predictive biomarker for NAMPT inhibitors.
abstract: OBJECTIVE
  We sought to identify predictive biomarkers for a novel nicotinamide phosphoribosyltransferase (NAMPT) inhibitor.
  
  
  METHODS
  We use a NAMPT inhibitor, GNE-617, to evaluate nicotinic acid rescue status in a panel of more than 400 cancer cell lines. Using correlative analysis and RNA interference (RNAi), we identify a specific biomarker for nicotinic acid rescue status. We next determine the mechanism of regulation of expression of the biomarker. Finally, we develop immunohistochemical (IHC) and DNA methylation assays and evaluate cancer tissue for prevalence of the biomarker across indications.
  
  
  RESULTS
  Nicotinate phosphoribosyltransferase (NAPRT1) is necessary for nicotinic acid rescue and its expression is the major determinant of rescue status. We demonstrate that NAPRT1 promoter methylation accounts for NAPRT1 deficiency in cancer cells, and NAPRT1 methylation is predictive of rescue status in cancer cell lines. Bisulfite next-generation sequencing mapping of the NAPRT1 promoter identified tumor-specific sites of NAPRT1 DNA methylation and enabled the development of a quantitative methylation-specific PCR (QMSP) assay suitable for use on archival formalin-fixed paraffin-embedded tumor tissue.
  
  
  CONCLUSIONS
  Tumor-specific promoter hypermethylation of NAPRT1 inactivates one of two NAD salvage pathways, resulting in synthetic lethality with the coadministration of a NAMPT inhibitor. NAPRT1 expression is lost due to promoter hypermethylation in most cancer types evaluated at frequencies ranging from 5% to 65%. NAPRT1-specific immunohistochemical or DNA methylation assays can be used on archival formalin paraffin-embedded cancer tissue to identify patients likely to benefit from coadministration of a Nampt inhibitor and nicotinic acid.
authors.affiliation: Authors' Affiliation: Genentech, Inc., South San Francisco, California.
authors.forename: David S
authors.initials: DS
authors.lastname: Shames
authors.forename: Kristi
authors.initials: K
authors.lastname: Elkins
authors.forename: Kimberly
authors.initials: K
authors.lastname: Walter
authors.forename: Thomas
authors.initials: T
authors.lastname: Holcomb
authors.forename: Pan
authors.initials: P
authors.lastname: Du
authors.forename: Dane
authors.initials: D
authors.lastname: Mohl
authors.forename: Yang
authors.initials: Y
authors.lastname: Xiao
authors.forename: Thinh
authors.initials: T
authors.lastname: Pham
authors.forename: Peter M
authors.initials: PM
authors.lastname: Haverty
authors.forename: Bianca
authors.initials: B
authors.lastname: Liederer
authors.forename: Xiaorong
authors.initials: X
authors.lastname: Liang
authors.forename: Robert L
authors.initials: RL
authors.lastname: Yauch
authors.forename: Thomas
authors.initials: T
authors.lastname: O'Brien
authors.forename: Richard
authors.initials: R
authors.lastname: Bourgon
authors.forename: Hartmut
authors.initials: H
authors.lastname: Koeppen
authors.forename: Lisa D
authors.initials: LD
authors.lastname: Belmont
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics; D045744:Cell Line, Tumor; D016207:Cytokines / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic; D006574:Heterocyclic Compounds, 2-Ring / Q000008:administration & dosage*; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D009525:Niacin / Q000008:administration & dosage / Q000378:metabolism*; D054409:Nicotinamide Phosphoribosyltransferase / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D010430:Pentosyltransferases / Q000037:antagonists & inhibitors / Q000172:deficiency / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D013450:Sulfones / Q000008:administration & dosage*
chemical_list: D014408:Biomarkers, Tumor; D016207:Cytokines; C000591022:GNE-617; D006574:Heterocyclic Compounds, 2-Ring; D013450:Sulfones; D009525:Niacin; D010430:Pentosyltransferases; D054409:Nicotinamide Phosphoribosyltransferase; C085455:nicotinamide phosphoribosyltransferase, human; C021864:nicotinate phosphoribosyltransferase